Dear Lalit,
Recently we published our work in JPC Letters, about the MD simulation
of adenosin receptor (GPCR) in membrane environemnt, at 0.15 and at 1.00
M NaCl concentration (Molecular Dynamics Simulation at High Sodium
Chloride Concentration: Toward the Inactive Conformation of the Human
Adenosine A2A Receptor - ASAP publication, doi: 10.1021/jz900403a). We
didn't performed simulation at 0 M (using only counter ions), but in our
cases we detected significant differences in the receptor structures,
trajectories in the different NaCl concentration.
The Jungwirth papers are very important, because they described at
first, that the effect of ions on protein structure is a direct
interactions between the ions and protein side chains. I would like to
suggest two other articles from Jungwirth, which are very important in
this field:
Ions at Aqueous Interfaces: FromWater Surface to Hydrated Proteins,
Pavel Jungwirth and Bernd Winter, Annu. Rev. Phys. Chem. 2008. 59:343–66.
Quantification and rationalization of the higher affinity of sodium over
potassium to protein surfaces, Vrbka et al, PNAS, 2006, 103(42):
15440–15444.
Hope this helps,
Balazs
Lalit Dubey wrote:
> Hi Watson and others,
>
> Many thanks for the paper list. I am following the papers from Pavel
> Jungwirth group.
>
> Moreover, I am very curious to hear thoughts of practitioners - the persons
> who do protein+Bilayer simulations and how they deal with salt concentration
> issue??
>
> Any thoughts will be highly appreciated.
>
> Thanks again,
> --- Lalit
>
>
>
> On Mon, Mar 1, 2010 at 9:03 AM, David Watson <dewatson.olemiss.edu> wrote:
>
>
>> On Mar 1, 2010, at 8:43 AM, Lalit Dubey wrote:
>>
>>
>>> Hi Jason,
>>>
>>> Thats truly the way to think about the role of ions in a protein+Bilayer
>>> simulation at first. Thanks. But whats the judgement or say, convention
>>>
>> as
>>
>>> of now. We can think of a 'protein' as a generic one. Nothing especial.
>>>
>> (All
>>
>>> polar residues are towards outside surface and hydrophobic ones
>>> are buried inside). [Mine is pkc with +1e charge].
>>>
>>> Whats the motivation for those who do protein + Bilayer simulations to
>>>
>> add
>>
>>> or just to not add salt concentration in the system??
>>>
>>> Mine was that it hardly matters in such a big system and contemporary
>>>
>> others
>>
>>> are not treating it (as a critical factor) and still doing
>>>
>> protein+Bilayer
>>
>>> simulations. Moreover, our experience with other similar systems shows
>>> little effect on salt concentration.[I am going to write individually to
>>>
>> all
>>
>>> those who have published such a work however I want initial motivation
>>> factors that makes the judgement at first].
>>>
>>> yeah, I have to address this question as raised in a seminar.
>>>
>>>
>> I remember reading (on this list, I believe) about detrimental effects of
>> too much salt, namely the salt "crystallizing" during the simulation.
>>
>> Here's a cherry-picked list of a quick SciFinder search
>>
>> Ion Specificity at the Peptide Bond: Molecular Dynamics Simulations of
>> N-Methylacetamide in Aqueous Salt Solutions
>> By Heyda, Jan; Vincent, Jordan C.; Tobias, Douglas J.; Dzubiella, Joachim;
>> Jungwirth, Pavel
>> From Journal of Physical Chemistry B (2010), 114(2), 1213-1220.
>>
>> Effect of counterions on the structure of reverse micelles according to the
>> data of molecular-dynamic simulation
>> By Mudzhikova, G. V.; Brodskaya, E. N.
>> From Colloid Journal (2009), 71(6), 803-809.
>>
>> Salt Dependence of an α-Helical Peptide Folding Energy Landscapes
>> By Xiong, Kan; Asciutto, Eliana K.; Madura, Jeffry D.; Asher, Sanford A.
>> From Biochemistry (2009), 48(45), 10818-10826.
>>
>> Molecular dynamics simulation of effect of salt on the compromise of
>> hydrophilic and hydrophobic interactions in sodium dodecyl sulfate micelle
>> solutions
>> By Gao, Jian; Ren, Ying; Ge, Wei
>> From Chinese Journal of Chemical Engineering (2009), 17(4), 654-660.
>>
>> Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane
>> By Vacha, Robert; Siu, Shirley W. I.; Petrov, Michal; Bockmann, Rainer A.;
>> Barucha-Kraszewska, Justyna; Jurkiewicz, Piotr; Hof, Martin; Berkowitz, Max
>> L.; Jungwirth, Pavel
>> From Journal of Physical Chemistry A (2009), 113(26), 7235-7243.
>>
>>
>>> Thanks again,
>>> --- Lalit
>>>
>>>
>>> On Sun, Feb 28, 2010 at 6:40 PM, Jason Swails <jason.swails.gmail.com
>>> wrote:
>>>
>>>
>>>> On Sun, Feb 28, 2010 at 6:35 PM, Lalit Dubey <dubey.lalit.gmail.com>
>>>> wrote:
>>>>
>>>>> Hello Florent,
>>>>>
>>>>> Thanks for the quick response!
>>>>>
>>>>> Yes, indeed putting counter ions to neutralize the whole system is
>>>>>
>>>> required
>>>>
>>>>> for full PME calculation of electrostatic forces.
>>>>> This part is fine. I have added counter ions. My systems are neutral.
>>>>>
>>>>> My question concerns with the effect of *'physiological concentration
>>>>>
>> of
>>
>>>>> salt'* (say, NaCl) on the configuration of protein.
>>>>>
>>>> Maybe yes, maybe no. Depends on your system. Evaluating even
>>>> classical laws on that number of interacting particles is inherently
>>>> chaotic and with the right set of variables anything can happen.
>>>>
>>>> Look for experimental data about your protein -- do they control the
>>>> salt concentration? Do they say what happens to the activity when
>>>> it's absent? Do they address it?
>>>>
>>>> I'm guessing if you're looking to publish this data, a reviewer may
>>>> ask that exact same question, and the only way of addressing it really
>>>> is to run those simulations. But again, maybe not if salt is known
>>>> not to be a large factor. All-in-all, this is a very long non-answer.
>>>> That's my $0.02.
>>>>
>>>> As a side note, when a system is not formally neutral, a "neutralizing
>>>> plasma". This is how, for instance, softcore potential TI is handled
>>>> when the net charge of the system changes (I'm pretty sure).
>>>>
>>>>
>>>> Good luck!
>>>> Jason
>>>>
>>>> --
>>>> ---------------------------------------
>>>> Jason M. Swails
>>>> Quantum Theory Project,
>>>> University of Florida
>>>> Ph.D. Graduate Student
>>>> 352-392-4032
>>>>
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Received on Wed Mar 03 2010 - 00:00:03 PST
